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Merge branch 'master' into package-reorganization2

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This commit is contained in:
Axel Kohlmeyer
2021-07-23 07:41:10 -04:00
parent f53c1978cc 8889fa316e
commit d2684a2370
334 changed files with 16639 additions and 18294 deletions
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2
examples/README
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@ -103,7 +103,7 @@ pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script
qeq: use of QEQ package for charge equilibration
reax: RDX and TATB and several other models using ReaxFF
reaxff: RDX and TATB and several other models using ReaxFF
rerun: use of rerun and read_dump commands
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void

22
examples/qeq/buck.inc Normal file
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@ -0,0 +1,22 @@
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve

75
examples/qeq/in.qeq.buck
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@ -1,41 +1,68 @@
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
replicate 2 2 2
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
group type1 type 1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot
thermo 10
timestep 0.0001
include buck.inc
velocity all create 300.0 1281937
fix 1 all nve
run 0 post no
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
write_restart qeq.restart
run 100
clear
print "Using fix qeq/point"
read_restart qeq.restart
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/shielded"
read_restart qeq.restart
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/slater"
read_restart qeq.restart
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/dynamic"
read_restart qeq.restart
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/fire"
read_restart qeq.restart
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
run 100

650
examples/qeq/log.20Apr21.qeq.buck.g++.1 Normal file
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@ -0,0 +1,650 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
read_data CPU = 0.009 seconds
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
velocity all create 300.0 1281937
run 0 post no
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.30705229
grid = 48 48 54
stencil order = 5
estimated absolute RMS force accuracy = 1.8909403e-05
estimated relative force accuracy = 1.3131854e-06
using double precision FFTW3
3d grid and FFT values/proc = 184525 124416
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Fix qeq CG convergence failed (4.357840257025601e-19) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
WARNING: Fix qeq CG convergence failed (5.274094378414531e-18) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
Per MPI rank memory allocation (min/avg/max) = 38.75 | 38.75 | 38.75 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00327 0.76536977 -0.38268489 0.000000000000 10
Loop time of 1.66893e-06 on 1 procs for 0 steps with 1200 atoms
write_restart qeq.restart
System init for write_restart ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/point"
Using fix qeq/point
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/point, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.17988 0.85228288 -0.42614144 -0.000000000000 3
10 -3452.03328 0.85475605 -0.42737803 -0.000000000000 8
20 -3497.57515 0.85994936 -0.42997468 0.000000000000 8
30 -3568.22095 0.86767937 -0.43383969 0.000000000001 8
40 -3633.24956 0.87335551 -0.43667775 0.000000000000 8
50 -3700.10219 0.87805056 -0.43902528 0.000000000000 8
60 -3784.36769 0.88402303 -0.44201151 -0.000000000000 8
70 -3877.51378 0.89008950 -0.44504475 0.000000000000 8
80 -3965.29722 0.89431515 -0.44715757 -0.000000000001 8
90 -4048.36764 0.89698588 -0.44849294 0.000000000000 8
100 -4118.65809 0.89719102 -0.44859551 0.000000000000 8
Loop time of 11.5935 on 1 procs for 100 steps with 1200 atoms
Performance: 0.075 ns/day, 322.041 hours/ns, 8.626 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8257 | 2.8257 | 2.8257 | 0.0 | 24.37
Kspace | 1.2136 | 1.2136 | 1.2136 | 0.0 | 10.47
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015541 | 0.015541 | 0.015541 | 0.0 | 0.13
Output | 0.0014489 | 0.0014489 | 0.0014489 | 0.0 | 0.01
Modify | 7.5351 | 7.5351 | 7.5351 | 0.0 | 64.99
Other | | 0.00206 | | | 0.02
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/shielded"
Using fix qeq/shielded
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 -0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 0.000000000001 1
40 -2942.24129 0.76536939 -0.38268470 -0.000000000001 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000001 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 7.93936 on 1 procs for 100 steps with 1200 atoms
Performance: 0.109 ns/day, 220.538 hours/ns, 12.595 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8061 | 2.8061 | 2.8061 | 0.0 | 35.34
Kspace | 1.2176 | 1.2176 | 1.2176 | 0.0 | 15.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015528 | 0.015528 | 0.015528 | 0.0 | 0.20
Output | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 0.02
Modify | 3.8966 | 3.8966 | 3.8966 | 0.0 | 49.08
Other | | 0.002076 | | | 0.03
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/slater"
Using fix qeq/slater
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 -0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 0.000000000001 1
40 -2942.24129 0.76536939 -0.38268470 -0.000000000001 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000001 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 7.9652 on 1 procs for 100 steps with 1200 atoms
Performance: 0.108 ns/day, 221.256 hours/ns, 12.555 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.809 | 2.809 | 2.809 | 0.0 | 35.27
Kspace | 1.2214 | 1.2214 | 1.2214 | 0.0 | 15.33
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015635 | 0.015635 | 0.015635 | 0.0 | 0.20
Output | 0.0014393 | 0.0014393 | 0.0014393 | 0.0 | 0.02
Modify | 3.9157 | 3.9157 | 3.9157 | 0.0 | 49.16
Other | | 0.002091 | | | 0.03
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/dynamic"
Using fix qeq/dynamic
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/dynamic, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.87 | 17.87 | 17.87 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.38094 0.85231286 -0.42615643 0.000000000001 43
10 -3452.05217 0.85475894 -0.42737947 -0.000000000001 17
20 -3497.8643 0.85999180 -0.42999590 -0.000000000007 22
30 -3568.53169 0.86772479 -0.43386239 -0.000000000006 22
40 -3633.43753 0.87338291 -0.43669146 -0.000000000006 22
50 -3700.27953 0.87807632 -0.43903816 -0.000000000005 22
60 -3784.4004 0.88402822 -0.44201411 0.000000000002 17
70 -3877.73706 0.89012201 -0.44506100 0.000000000002 22
80 -3965.36111 0.89432486 -0.44716243 0.000000000008 17
90 -4048.57901 0.89701688 -0.44850844 -0.000000000004 22
100 -4118.62736 0.89718691 -0.44859346 -0.000000000026 17
Loop time of 18.5333 on 1 procs for 100 steps with 1200 atoms
Performance: 0.047 ns/day, 514.815 hours/ns, 5.396 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8268 | 2.8268 | 2.8268 | 0.0 | 15.25
Kspace | 1.2138 | 1.2138 | 1.2138 | 0.0 | 6.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015407 | 0.015407 | 0.015407 | 0.0 | 0.08
Output | 0.0014303 | 0.0014303 | 0.0014303 | 0.0 | 0.01
Modify | 14.474 | 14.474 | 14.474 | 0.0 | 78.10
Other | | 0.001973 | | | 0.01
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/fire"
Using fix qeq/fire
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.87 | 17.87 | 17.87 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.06113 0.85226679 -0.42613339 0.000000000004 37
10 -3452.0494 0.85475813 -0.42737906 0.000000000001 10
20 -3497.83503 0.85998739 -0.42999370 0.000000000003 13
30 -3568.47507 0.86771599 -0.43385799 0.000000000004 13
40 -3633.35368 0.87337029 -0.43668514 0.000000000004 13
50 -3700.15601 0.87805847 -0.43902924 0.000000000005 13
60 -3784.32042 0.88401635 -0.44200818 0.000000000000 11
70 -3877.59818 0.89010162 -0.44505081 0.000000000000 13
80 -3965.28426 0.89431356 -0.44715678 0.000000000000 11
90 -4048.3338 0.89698069 -0.44849034 0.000000000001 13
100 -4118.63638 0.89718818 -0.44859409 0.000000000003 12
Loop time of 13.0492 on 1 procs for 100 steps with 1200 atoms
Performance: 0.066 ns/day, 362.479 hours/ns, 7.663 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7996 | 2.7996 | 2.7996 | 0.0 | 21.45
Kspace | 1.2141 | 1.2141 | 1.2141 | 0.0 | 9.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015527 | 0.015527 | 0.015527 | 0.0 | 0.12
Output | 0.0014405 | 0.0014405 | 0.0014405 | 0.0 | 0.01
Modify | 9.0166 | 9.0166 | 9.0166 | 0.0 | 69.10
Other | | 0.001981 | | | 0.02
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:00

650
examples/qeq/log.20Apr21.qeq.buck.g++.4 Normal file
View File

@ -0,0 +1,650 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
reading atoms ...
1200 atoms
read_data CPU = 0.009 seconds
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
velocity all create 300.0 1281937
run 0 post no
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.30705229
grid = 48 48 54
stencil order = 5
estimated absolute RMS force accuracy = 1.8909403e-05
estimated relative force accuracy = 1.3131854e-06
using double precision FFTW3
3d grid and FFT values/proc = 57970 32256
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Fix qeq CG convergence failed (4.299911728887494e-19) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
WARNING: Fix qeq CG convergence failed (5.273380778822746e-18) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
Per MPI rank memory allocation (min/avg/max) = 14.97 | 15.02 | 15.08 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00327 0.76536977 -0.38268489 0.000000000000 10
Loop time of 3.33786e-06 on 4 procs for 0 steps with 1200 atoms
write_restart qeq.restart
System init for write_restart ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/point"
Using fix qeq/point
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/point, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.17988 0.85228288 -0.42614144 -0.000000000000 3
10 -3452.03328 0.85475605 -0.42737803 -0.000000000000 8
20 -3497.57515 0.85994936 -0.42997468 0.000000000000 8
30 -3568.22095 0.86767937 -0.43383969 0.000000000000 8
40 -3633.24956 0.87335551 -0.43667775 -0.000000000000 8
50 -3700.10219 0.87805056 -0.43902528 0.000000000000 8
60 -3784.36769 0.88402303 -0.44201151 0.000000000000 8
70 -3877.51378 0.89008950 -0.44504475 0.000000000000 8
80 -3965.29722 0.89431515 -0.44715757 0.000000000000 8
90 -4048.36764 0.89698588 -0.44849294 -0.000000000000 8
100 -4118.65809 0.89719102 -0.44859551 0.000000000000 8
Loop time of 3.30911 on 4 procs for 100 steps with 1200 atoms
Performance: 0.261 ns/day, 91.920 hours/ns, 30.220 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67613 | 0.68904 | 0.71562 | 1.9 | 20.82
Kspace | 0.36056 | 0.3881 | 0.39892 | 2.6 | 11.73
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013339 | 0.017982 | 0.019974 | 2.0 | 0.54
Output | 0.0006721 | 0.00099713 | 0.0019572 | 0.0 | 0.03
Modify | 2.2109 | 2.211 | 2.211 | 0.0 | 66.81
Other | | 0.002041 | | | 0.06
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/shielded"
Using fix qeq/shielded
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.006 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 -0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 -0.000000000000 1
40 -2942.24129 0.76536939 -0.38268470 0.000000000000 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 -0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000000 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 2.25559 on 4 procs for 100 steps with 1200 atoms
Performance: 0.383 ns/day, 62.655 hours/ns, 44.334 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67442 | 0.69181 | 0.70907 | 2.0 | 30.67
Kspace | 0.39381 | 0.41151 | 0.43023 | 2.6 | 18.24
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012851 | 0.01426 | 0.015146 | 0.7 | 0.63
Output | 0.00066686 | 0.00098681 | 0.0019395 | 0.0 | 0.04
Modify | 1.1349 | 1.135 | 1.135 | 0.0 | 50.32
Other | | 0.002035 | | | 0.09
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/slater"
Using fix qeq/slater
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.012 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 -0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 -0.000000000000 1
40 -2942.24129 0.76536939 -0.38268470 0.000000000000 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 -0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000000 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 2.39249 on 4 procs for 100 steps with 1200 atoms
Performance: 0.361 ns/day, 66.458 hours/ns, 41.797 timesteps/s
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.6751 | 0.70301 | 0.71919 | 2.1 | 29.38
Kspace | 0.45569 | 0.47315 | 0.49885 | 2.6 | 19.78
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012967 | 0.018681 | 0.020909 | 2.4 | 0.78
Output | 0.00066733 | 0.00099397 | 0.0019579 | 0.0 | 0.04
Modify | 1.1945 | 1.1946 | 1.1947 | 0.0 | 49.93
Other | | 0.002046 | | | 0.09
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/dynamic"
Using fix qeq/dynamic
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.002 seconds
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/dynamic, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.195 | 9.246 | 9.278 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.38094 0.85231286 -0.42615643 -0.000000000001 43
10 -3452.05217 0.85475894 -0.42737947 -0.000000000003 17
20 -3497.8643 0.85999180 -0.42999590 0.000000000000 22
30 -3568.53169 0.86772479 -0.43386239 -0.000000000000 22
40 -3633.43753 0.87338291 -0.43669146 0.000000000006 22
50 -3700.27953 0.87807632 -0.43903816 0.000000000003 22
60 -3784.4004 0.88402822 -0.44201411 0.000000000009 17
70 -3877.73706 0.89012201 -0.44506100 0.000000000010 22
80 -3965.36111 0.89432486 -0.44716243 0.000000000011 17
90 -4048.57901 0.89701688 -0.44850844 0.000000000012 22
100 -4118.62736 0.89718691 -0.44859346 0.000000000013 17
Loop time of 5.27704 on 4 procs for 100 steps with 1200 atoms
Performance: 0.164 ns/day, 146.584 hours/ns, 18.950 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.68437 | 0.69096 | 0.69826 | 0.7 | 13.09
Kspace | 0.38484 | 0.38941 | 0.39524 | 0.7 | 7.38
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012609 | 0.01529 | 0.016842 | 1.3 | 0.29
Output | 0.00067735 | 0.0010006 | 0.0019588 | 1.7 | 0.02
Modify | 4.1783 | 4.1783 | 4.1784 | 0.0 | 79.18
Other | | 0.002027 | | | 0.04
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 93081 max 90719 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/fire"
Using fix qeq/fire
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.195 | 9.246 | 9.278 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.05316 0.85226679 -0.42613339 0.000000000001 37
10 -3452.04937 0.85475813 -0.42737906 0.000000000001 10
20 -3497.83659 0.85998739 -0.42999370 0.000000000002 13
30 -3568.47793 0.86771599 -0.43385799 0.000000000002 13
40 -3633.35326 0.87337029 -0.43668514 0.000000000002 13
50 -3700.16079 0.87805847 -0.43902924 0.000000000000 13
60 -3784.31906 0.88401635 -0.44200818 -0.000000000001 11
70 -3877.60163 0.89010162 -0.44505081 -0.000000000000 13
80 -3965.28179 0.89431356 -0.44715678 0.000000000001 11
90 -4048.33861 0.89698069 -0.44849034 0.000000000001 13
100 -4118.63861 0.89718818 -0.44859409 0.000000000002 12
Loop time of 3.88026 on 4 procs for 100 steps with 1200 atoms
Performance: 0.223 ns/day, 107.785 hours/ns, 25.771 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.68424 | 0.69912 | 0.73572 | 2.5 | 18.02
Kspace | 0.38093 | 0.41715 | 0.43168 | 3.2 | 10.75
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012711 | 0.013318 | 0.014003 | 0.4 | 0.34
Output | 0.00066566 | 0.00098735 | 0.0019317 | 0.0 | 0.03
Modify | 2.7477 | 2.7477 | 2.7477 | 0.0 | 70.81
Other | | 0.002004 | | | 0.05
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 93081 max 90719 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:17

118
examples/qeq/log.27Nov18.qeq.buck.g++.1
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
replicate 2 2 2
orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
1 by 1 by 1 MPI processor grid
9600 atoms
Time spent = 0.00114894 secs
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
3200 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
6400 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
thermo 10
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
run 100
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 13556 20 34460
kxmax kymax kzmax = 18 18 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 8 8 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 134 | 134 | 134 Mbytes
Step PotEng c_q1 c_q2 v_qtot S/CPU
0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0
10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64313877
20 -27975.085 0.85968531 -0.42984266 -1.036824e-10 0.55119179
30 -28552.628 0.86755661 -0.4337783 1.3051249e-10 0.53160643
40 -29133.643 0.87426387 -0.43713193 1.1368684e-10 0.53075341
50 -29697.011 0.8794039 -0.43970195 1.200533e-10 0.52358127
60 -30342.001 0.88478594 -0.44239297 6.002665e-11 0.5366762
70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.55904546
80 -31792.732 0.89506635 -0.44753317 -4.3200998e-11 0.59606079
90 -32424.749 0.89714841 -0.44857421 -1.1596057e-10 0.58047419
100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59444001
Loop time of 177.79 on 1 procs for 100 steps with 9600 atoms
Performance: 0.005 ns/day, 4938.612 hours/ns, 0.562 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.518 | 11.518 | 11.518 | 0.0 | 6.48
Kspace | 107.37 | 107.37 | 107.37 | 0.0 | 60.39
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019721 | 0.019721 | 0.019721 | 0.0 | 0.01
Output | 0.002218 | 0.002218 | 0.002218 | 0.0 | 0.00
Modify | 58.869 | 58.869 | 58.869 | 0.0 | 33.11
Other | | 0.007197 | | | 0.00
Nlocal: 9600 ave 9600 max 9600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22125 ave 22125 max 22125 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.9408e+06 ave 2.9408e+06 max 2.9408e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2940800
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:01

118
examples/qeq/log.27Nov18.qeq.buck.g++.4
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 2 by 2 MPI processor grid
reading atoms ...
1200 atoms
replicate 2 2 2
orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
1 by 2 by 2 MPI processor grid
9600 atoms
Time spent = 0.000675201 secs
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
3200 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
6400 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
thermo 10
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
run 100
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 13556 20 34460
kxmax kymax kzmax = 18 18 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 8 8 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 53.06 | 53.13 | 53.21 Mbytes
Step PotEng c_q1 c_q2 v_qtot S/CPU
0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0
10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.4245312
20 -27975.085 0.85968531 -0.42984266 1.0095391e-10 2.0185316
30 -28552.627 0.86755661 -0.4337783 1.3096724e-10 1.9605335
40 -29133.643 0.87426387 -0.43713193 1.5279511e-10 1.9624139
50 -29697.01 0.8794039 -0.43970195 1.6461854e-10 1.8113263
60 -30342 0.88478594 -0.44239297 1.7826096e-10 1.9537722
70 -31081.139 0.89069733 -0.44534866 1.4733814e-10 2.058406
80 -31792.732 0.89506635 -0.44753317 1.3824319e-10 2.2160813
90 -32424.752 0.89714841 -0.44857421 1.2914825e-10 2.0952145
100 -32998.353 0.89755721 -0.44877861 1.4824764e-10 2.1292486
Loop time of 48.7541 on 4 procs for 100 steps with 9600 atoms
Performance: 0.018 ns/day, 1354.281 hours/ns, 2.051 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9747 | 3.0315 | 3.0758 | 2.1 | 6.22
Kspace | 27.873 | 28.264 | 28.63 | 5.3 | 57.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.53835 | 0.8523 | 1.2286 | 28.2 | 1.75
Output | 0.0012984 | 0.001591 | 0.0024178 | 1.2 | 0.00
Modify | 16.58 | 16.59 | 16.601 | 0.3 | 34.03
Other | | 0.01409 | | | 0.03
Nlocal: 2400 ave 2400 max 2400 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 11550 ave 11550 max 11550 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 735200 ave 740758 max 729642 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2940800
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:49

1
examples/qeq/param.qeq1
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@ -1,3 +1,4 @@
# UNITS: real
1 5.3200 14.8732 1.0206 0.0 0.0
2 5.8678 14.0000 0.9000 0.0 0.0
3 8.5000 17.9978 1.0503 0.0 0.0

1
examples/qeq/param.qeq2
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@ -1,2 +1,3 @@
# UNITS: metal
1 0.00000 7.25028 0.01 0.772871 0.000000
2 11.26882 15.37920 0.01 0.243072 0.000000

52
examples/reax/in.reaxc.rdx
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# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100

52
examples/reax/in.reaxc.rdx-shielded
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# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100

55
examples/reax/in.reaxc.tatb
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@ -1,55 +0,0 @@
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25

55
examples/reax/in.reaxc.tatb-shielded
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@ -1,55 +0,0 @@
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25

116
examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1
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LAMMPS (4 Jan 2019)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.54 | 15.54 | 15.54 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79939 0 168.88404
10 1288.6115 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.1252289 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
20 538.95832 -1942.7037 -1910.5731 -10725.665 -2803.7395 7.9078296 0.077926657 0 81.61005 0.22951928 -57.5571 0 30.331204 -10.178049 878.99014 -159.69088 0 89.31512
30 463.09535 -1933.5765 -1905.9685 -33255.521 -2749.8591 -8.0154561 0.027628873 0 81.62739 0.11972409 -50.262289 0 20.820315 -9.6327029 851.88723 -149.49502 0 79.205749
40 885.49232 -1958.9126 -1906.1229 -4814.704 -2795.644 9.1506683 0.13747502 0 70.947988 0.2436053 -57.862679 0 19.076499 -11.141216 873.73896 -159.99392 0 92.434085
50 861.16622 -1954.4599 -1903.1204 -1896.7878 -2784.8448 3.8269901 0.15793272 0 79.851828 3.3492155 -78.066128 0 32.628996 -7.9565333 872.81832 -190.98567 0 114.75995
60 1167.7852 -1971.843 -1902.2241 -3482.6875 -2705.8632 -17.121673 0.22749075 0 44.507672 7.856086 -74.788945 0 16.256491 -4.6046463 835.83056 -188.33693 0 114.19414
70 1439.997 -1989.3024 -1903.4553 23845.434 -2890.7895 31.958869 0.26671726 0 85.758681 3.1803462 -71.002898 0 24.35711 -10.311314 905.86781 -175.38471 0 106.79648
80 502.39629 -1930.7545 -1900.8035 -20356.384 -2703.8111 -18.66263 0.11286065 0 99.804114 2.0329076 -76.171338 0 19.23692 -6.2786691 826.47429 -166.03132 0 92.539464
90 749.08722 -1946.9837 -1902.3259 17798.557 -2863.7579 42.068808 0.24338058 0 96.181716 0.96183793 -69.955449 0 24.615308 -11.58277 903.68837 -190.13841 0 120.6914
100 1109.6997 -1968.5874 -1902.4313 -4490.2776 -2755.896 -7.1232734 0.21757686 0 61.806176 7.0827207 -75.645383 0 20.114879 -6.2371839 863.56324 -198.56967 0 122.09951
Loop time of 0.657427 on 1 procs for 100 steps with 21 atoms
Performance: 13.142 ns/day, 1.826 hours/ns, 152.108 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.59308 | 0.59308 | 0.59308 | 0.0 | 90.21
Neigh | 0.020665 | 0.020665 | 0.020665 | 0.0 | 3.14
Comm | 0.0015757 | 0.0015757 | 0.0015757 | 0.0 | 0.24
Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.06
Modify | 0.04156 | 0.04156 | 0.04156 | 0.0 | 6.32
Other | | 0.000154 | | | 0.02
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1306 ave 1306 max 1306 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1306
Ave neighs/atom = 62.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

116
examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4
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LAMMPS (4 Jan 2019)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.62 | 12.08 | 13.84 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79987 0 168.88452
10 1288.6116 -1989.6644 -1912.8422 -19456.355 -2734.6769 -15.60722 0.2017796 0 54.629559 3.1252284 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
20 538.95818 -1942.7037 -1910.5731 -10725.629 -2803.7394 7.9078295 0.077926694 0 81.61005 0.22951941 -57.557106 0 30.331206 -10.178049 878.9901 -159.68969 0 89.313929
30 463.09529 -1933.5765 -1905.9685 -33255.529 -2749.859 -8.0154758 0.027628845 0 81.627406 0.1197241 -50.26229 0 20.82031 -9.6327013 851.88715 -149.49497 0 79.205706
40 885.49462 -1958.9125 -1906.1227 -4814.6528 -2795.6439 9.1506212 0.13747486 0 70.94804 0.24360501 -57.862675 0 19.076509 -11.141214 873.7389 -159.99391 0 92.434076
50 861.16112 -1954.4601 -1903.121 -1896.6704 -2784.8452 3.8270543 0.15793292 0 79.851662 3.3492078 -78.066133 0 32.628979 -7.9565431 872.81857 -190.9857 0 114.75999
60 1167.7837 -1971.8434 -1902.2245 -3482.8961 -2705.8635 -17.121601 0.22749083 0 44.507696 7.8559922 -74.789025 0 16.256492 -4.6046625 835.83053 -188.33688 0 114.19412
70 1439.9917 -1989.3024 -1903.4555 23845.887 -2890.7894 31.958677 0.26671714 0 85.758424 3.1804092 -71.002955 0 24.357221 -10.311284 905.86805 -175.38496 0 106.7967
80 502.39695 -1930.7548 -1900.8039 -20356.331 -2703.8113 -18.662598 0.11286102 0 99.803743 2.0329429 -76.171299 0 19.236922 -6.2786652 826.4744 -166.03139 0 92.539525
90 749.08478 -1946.984 -1902.3264 17798.605 -2863.7581 42.068587 0.24338052 0 96.181622 0.96184063 -69.955519 0 24.615456 -11.582749 903.68853 -190.13827 0 120.69126
100 1109.6952 -1968.5879 -1902.4321 -4490.2728 -2755.8985 -7.1225966 0.21757682 0 61.805902 7.0826502 -75.64544 0 20.115369 -6.2372513 863.56451 -198.56956 0 122.09944
Loop time of 0.634333 on 4 procs for 100 steps with 21 atoms
Performance: 13.621 ns/day, 1.762 hours/ns, 157.646 timesteps/s
93.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53395 | 0.5352 | 0.53805 | 0.2 | 84.37
Neigh | 0.0088253 | 0.012023 | 0.016203 | 2.4 | 1.90
Comm | 0.0051677 | 0.0081 | 0.0093861 | 1.9 | 1.28
Output | 0.00049353 | 0.00054371 | 0.00058222 | 0.0 | 0.09
Modify | 0.074155 | 0.078299 | 0.081472 | 0.9 | 12.34
Other | | 0.0001715 | | | 0.03
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
FullNghs: 326.5 ave 927 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1306
Ave neighs/atom = 62.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

114
examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.1
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LAMMPS (4 Jan 2019)
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 169.6 | 169.6 | 169.6 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274
5 0.61603942 -44761.698 -44760.994 8934.628 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691
10 2.3525549 -44763.227 -44760.541 12288.614 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9684 0 6381.7061
15 4.9013311 -44766.36 -44760.764 17716.982 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2449 0 6370.4111
20 7.8294673 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5142 0 6355.2654
25 10.697904 -44772.904 -44760.691 34232.821 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3541 0 6336.8349
Loop time of 7.80985 on 1 procs for 25 steps with 384 atoms
Performance: 0.017 ns/day, 1388.418 hours/ns, 3.201 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.003 | 5.003 | 5.003 | 0.0 | 64.06
Neigh | 1.1164 | 1.1164 | 1.1164 | 0.0 | 14.29
Comm | 0.0065806 | 0.0065806 | 0.0065806 | 0.0 | 0.08
Output | 0.00029969 | 0.00029969 | 0.00029969 | 0.0 | 0.00
Modify | 1.6831 | 1.6831 | 1.6831 | 0.0 | 21.55
Other | | 0.0004976 | | | 0.01
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 336304 ave 336304 max 336304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.792
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:08

114
examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.4
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LAMMPS (4 Jan 2019)
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 113 | 113 | 113 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277
5 0.61603968 -44761.698 -44760.994 8934.6336 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666
10 2.3525543 -44763.227 -44760.541 12288.588 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9756 0 6381.7133
15 4.9013233 -44766.36 -44760.764 17716.934 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2627 0 6370.4289
20 7.8294615 -44769.686 -44760.747 25205.586 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4958 0 6355.2471
25 10.697919 -44772.904 -44760.691 34232.898 -61069.308 490.25887 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3285 0 6336.8093
Loop time of 4.34178 on 4 procs for 25 steps with 384 atoms
Performance: 0.031 ns/day, 771.872 hours/ns, 5.758 timesteps/s
96.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1756 | 3.1763 | 3.1771 | 0.0 | 73.16
Neigh | 0.58917 | 0.59661 | 0.6035 | 0.9 | 13.74
Comm | 0.0088837 | 0.010178 | 0.011116 | 0.8 | 0.23
Output | 0.00036407 | 0.0019013 | 0.003552 | 2.7 | 0.04
Modify | 0.54882 | 0.55637 | 0.56413 | 0.8 | 12.81
Other | | 0.0004123 | | | 0.01
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 84076 ave 84076 max 84076 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.792
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

115
examples/reax/log.8March18.reaxc.rdx.g++.1
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 15.28 | 15.28 | 15.28 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79937 0 168.88402
10 1288.6114 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252294 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43322 0 107.75935
20 538.95849 -1942.7037 -1910.5731 -10725.658 -2803.7395 7.9078331 0.077926702 0 81.610043 0.22951937 -57.557104 0 30.331203 -10.178049 878.99015 -159.69092 0 89.315159
30 463.09542 -1933.5765 -1905.9685 -33255.507 -2749.8591 -8.0154628 0.027628767 0 81.627403 0.11972403 -50.262284 0 20.82032 -9.6327022 851.88722 -149.495 0 79.205731
40 885.49449 -1958.9126 -1906.1228 -4814.7123 -2795.644 9.1506221 0.1374749 0 70.948046 0.24360579 -57.8627 0 19.076515 -11.141211 873.73892 -159.9939 0 92.434059
50 861.1646 -1954.4599 -1903.1206 -1896.7387 -2784.8446 3.8269113 0.1579328 0 79.851775 3.3492107 -78.066127 0 32.628975 -7.9565255 872.81826 -190.98565 0 114.75994
60 1167.785 -1971.8432 -1902.2243 -3482.6975 -2705.8638 -17.121582 0.22749067 0 44.507705 7.856069 -74.788959 0 16.256519 -4.6046602 835.8308 -188.33691 0 114.19414
70 1439.9947 -1989.3024 -1903.4554 23845.067 -2890.7896 31.958874 0.26671735 0 85.758608 3.1803486 -71.002907 0 24.357106 -10.311315 905.86799 -175.38482 0 106.79659
80 502.40024 -1930.7547 -1900.8035 -20356.557 -2703.8096 -18.663105 0.11286226 0 99.803799 2.0329394 -76.171387 0 19.236609 -6.2786041 826.47358 -166.03157 0 92.539694
90 749.09267 -1946.9834 -1902.3254 17798.812 -2863.7586 42.068927 0.24338042 0 96.18195 0.96181754 -69.955528 0 24.61541 -11.58277 903.68895 -190.13838 0 120.69139
100 1109.7046 -1968.5875 -1902.4311 -4490.6736 -2755.8953 -7.1235173 0.21757663 0 61.806405 7.0825933 -75.645487 0 20.114745 -6.2371664 863.56285 -198.56939 0 122.09923
Loop time of 0.395195 on 1 procs for 100 steps with 21 atoms
Performance: 21.863 ns/day, 1.098 hours/ns, 253.039 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.3722 | 0.3722 | 0.3722 | 0.0 | 94.18
Neigh | 0.0098455 | 0.0098455 | 0.0098455 | 0.0 | 2.49
Comm | 0.00047445 | 0.00047445 | 0.00047445 | 0.0 | 0.12
Output | 0.00034022 | 0.00034022 | 0.00034022 | 0.0 | 0.09
Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 3.08
Other | | 0.0001521 | | | 0.04
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

115
examples/reax/log.8March18.reaxc.rdx.g++.4
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@ -1,115 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.37 | 11.76 | 13.34 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79988 0 168.88453
10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252286 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
20 538.95818 -1942.7037 -1910.5731 -10725.623 -2803.7394 7.9078307 0.077926702 0 81.61005 0.22951942 -57.557107 0 30.331206 -10.178049 878.9901 -159.68951 0 89.313749
30 463.09514 -1933.5765 -1905.9685 -33255.525 -2749.859 -8.0154737 0.027628797 0 81.627408 0.11972402 -50.262283 0 20.82031 -9.6327021 851.88715 -149.49499 0 79.205724
40 885.49412 -1958.9125 -1906.1227 -4814.6606 -2795.6439 9.150622 0.13747487 0 70.948029 0.24360517 -57.862679 0 19.076509 -11.141214 873.7389 -159.99392 0 92.434078
50 861.16393 -1954.46 -1903.1207 -1896.7323 -2784.8449 3.8270197 0.1579328 0 79.851743 3.3492115 -78.066132 0 32.628992 -7.9565379 872.81841 -190.98568 0 114.75996
60 1167.7846 -1971.8432 -1902.2243 -3482.8111 -2705.8633 -17.121657 0.2274907 0 44.507681 7.8560366 -74.788989 0 16.256493 -4.6046537 835.8305 -188.33687 0 114.1941
70 1439.9942 -1989.3023 -1903.4554 23845.444 -2890.7894 31.958784 0.26671721 0 85.758586 3.1803655 -71.002918 0 24.357158 -10.311304 905.86792 -175.38481 0 106.79657
80 502.3975 -1930.7546 -1900.8036 -20356.439 -2703.8105 -18.662812 0.11286123 0 99.80391 2.0329293 -76.171334 0 19.236803 -6.2786439 826.47397 -166.03141 0 92.539551
90 749.09048 -1946.9837 -1902.3258 17798.718 -2863.7582 42.068719 0.24338057 0 96.181773 0.96183581 -69.955529 0 24.615414 -11.582758 903.68862 -190.1384 0 120.69139
100 1109.6999 -1968.5875 -1902.4314 -4490.3728 -2755.8964 -7.1231468 0.21757685 0 61.806149 7.0826648 -75.645428 0 20.115002 -6.2371958 863.56343 -198.56957 0 122.09942
Loop time of 0.329552 on 4 procs for 100 steps with 21 atoms
Performance: 26.217 ns/day, 0.915 hours/ns, 303.443 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26372 | 0.26499 | 0.26754 | 0.3 | 80.41
Neigh | 0.0045478 | 0.0062494 | 0.0076699 | 1.5 | 1.90
Comm | 0.0041637 | 0.0064691 | 0.0080271 | 1.8 | 1.96
Output | 0.00054169 | 0.00056636 | 0.00060368 | 0.0 | 0.17
Modify | 0.049433 | 0.051134 | 0.05311 | 0.6 | 15.52
Other | | 0.000141 | | | 0.04
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.9048
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

113
examples/reax/log.8March18.reaxc.tatb.g++.1
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@ -1,113 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 176.7 | 176.7 | 176.7 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275
5 0.61603968 -44761.698 -44760.994 8934.6347 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671
10 2.3525551 -44763.227 -44760.541 12288.583 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9768 0 6381.7146
15 4.9013279 -44766.36 -44760.764 17717.01 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2375 0 6370.4038
20 7.8294645 -44769.686 -44760.747 25205.624 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4889 0 6355.2402
25 10.697904 -44772.904 -44760.691 34232.965 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3125 0 6336.7934
Loop time of 4.72562 on 1 procs for 25 steps with 384 atoms
Performance: 0.029 ns/day, 840.110 hours/ns, 5.290 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.775 | 3.775 | 3.775 | 0.0 | 79.88
Neigh | 0.47047 | 0.47047 | 0.47047 | 0.0 | 9.96
Comm | 0.0025151 | 0.0025151 | 0.0025151 | 0.0 | 0.05
Output | 0.0003159 | 0.0003159 | 0.0003159 | 0.0 | 0.01
Modify | 0.47676 | 0.47676 | 0.47676 | 0.0 | 10.09
Other | | 0.0005293 | | | 0.01
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.948
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05

113
examples/reax/log.8March18.reaxc.tatb.g++.4
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@ -1,113 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 118 | 118 | 118 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277
5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666
10 2.3525544 -44763.227 -44760.541 12288.587 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9764 0 6381.7141
15 4.9013311 -44766.36 -44760.764 17716.955 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2558 0 6370.4221
20 7.8294715 -44769.686 -44760.747 25205.613 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4906 0 6355.2419
25 10.697924 -44772.904 -44760.691 34232.794 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91376 -1582.3261 253.82253 -653.53183 18791.975 -8684.3641 0 6336.8449
Loop time of 2.84068 on 4 procs for 25 steps with 384 atoms
Performance: 0.048 ns/day, 505.009 hours/ns, 8.801 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3253 | 2.328 | 2.3305 | 0.2 | 81.95
Neigh | 0.2589 | 0.26458 | 0.26897 | 0.7 | 9.31
Comm | 0.0094428 | 0.012062 | 0.014872 | 2.3 | 0.42
Output | 0.00043392 | 0.0042209 | 0.0054941 | 3.4 | 0.15
Modify | 0.22563 | 0.23134 | 0.23579 | 0.8 | 8.14
Other | | 0.0005122 | | | 0.02
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.771
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

0
examples/reax/AB/README → examples/reaxff/AB/README
View File

0
examples/reax/AB/data.AB → examples/reaxff/AB/data.AB
View File

0
examples/reax/AB/ffield.reax.AB → examples/reaxff/AB/ffield.reax.AB
View File

0
examples/reax/AB/in.AB → examples/reaxff/AB/in.AB
View File

0
examples/reax/AB/lmp_control → examples/reaxff/AB/lmp_control
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